Lab 5x

Interactive Graph example

ggplotly(
  time_series_long_joined %>% 
    group_by(Country_Region,Date) %>% 
    summarise_at(c("Confirmed", "Deaths"), sum) %>% 
    filter (Country_Region == "US") %>% 
    ggplot(aes(x = Date,  y = Deaths)) + 
      geom_point() +
      geom_line() +
      ggtitle("US COVID-19 Deaths")
 )

Animated Graph example

library(gganimate)
library(transformr)
library(gifski)
theme_set(theme_bw())

data_time <- time_series_long_joined %>% 
    group_by(Country_Region,Date) %>% 
    summarise_at(c("Confirmed", "Deaths"), sum) %>% 
    filter (Country_Region %in% c("China","Korea, South","Japan","Italy","US")) 
p <- ggplot(data_time, aes(x = Date,  y = Confirmed, color = Country_Region)) + 
      geom_point() +
      geom_line() +
      ggtitle("Confirmed COVID-19 Cases") +
      geom_point(aes(group = seq_along(Date))) +
      transition_reveal(Date) 
# Some people needed to use this line instead
# animate(p,renderer = gifski_renderer(), end_pause = 15)
animate(p, end_pause = 15)

#

Challenge 1

Print a graph (different from the one above) to a png file using 3*ppi for the height and width and display the png file in the report using the above R Markdown format.

#Convert to PNG
ppi <- 200
png("images/time_series_example_plot.png", width=3*ppi, height=3*ppi, res=ppi)
time_series_long_joined %>% 
  group_by(Country_Region,Date) %>% 
  summarise_at(c("Confirmed", "Deaths"), sum) %>% 
  filter (Country_Region == "Brazil") %>% 
    ggplot(aes(x = Date,  y = Deaths)) + 
    geom_point() +
    geom_line() +
    ggtitle("Brazil COVID-19 Deaths")
dev.off()

## png 
##   2

Challenge 2

Turn one of the exercises from Lab 5 into an interactive graph with plotyly

time_series_long_joined_ratio <- time_series_long_joined %>% 
  group_by(Country_Region, Date) %>% 
  summarise(Total_Confirmed = sum(Confirmed), Total_Deaths = sum(Deaths)) %>%
  mutate(Ratio = Total_Deaths / Total_Confirmed)

time_series_long_total_deaths <- time_series_long_joined_ratio %>%
  group_by(Country_Region) %>%
  summarise(Deaths = sum(Total_Deaths)) %>%
  arrange(desc(Deaths)) %>%
  slice(1:10)

g <- time_series_long_joined_ratio %>% 
    filter(Country_Region %in% c("US", "Brazil", "United Kingdom", "Italy", "Mexico", "France", "Spain", "India", "Iran", "Peru")) %>% 
    ggplot(aes(x = Date,  y = Total_Deaths, fill = Country_Region, color = Country_Region)) + 
    geom_point() +
    geom_line() +
    ggtitle("The Top 10 Countries by Total Deaths") +
    transition_reveal(Date) 

animate(g,renderer = gifski_renderer(), end_pause = 15)

Challenge 3

Create an animated graph of your choosing using the time series data to display an aspect (e.g. states or countries) of the data that is important to you.

#Data Wrangling
download.file(url="https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv", destfile = "data/time_series_covid19_confirmed_US.csv")

time_series_covid19_confirmed_US <- read.csv("data/time_series_covid19_confirmed_US.csv")

time_series_covid19_confirmed_US_totals <- time_series_covid19_confirmed_US %>% select(-c(UID,iso2,iso3,code3,FIPS,Lat,Long_,Combined_Key,Admin2,Country_Region)) %>%  group_by(Province_State) %>%  summarise_each(funs(sum)) 

time_series_covid19_confirmed_US_totals <- time_series_covid19_confirmed_US_totals %>% rename_at(vars(starts_with("X")), funs(str_remove(., "X")))
  
confirmed_US_totals_long <- time_series_covid19_confirmed_US_totals %>%  pivot_longer(-c(Province_State), names_to = "Date", values_to = "Confirmed")
confirmed_US_totals_long$Date <- as.Date(confirmed_US_totals_long$Date, format = "%m.%d.%y")

ten_highest_confirmed_df <- confirmed_US_totals_long %>% 
  group_by(Province_State) %>% 
  summarise("Confirmed_Total"= sum(Confirmed)) %>% 
  arrange(desc(Confirmed_Total)) %>% 
  head(10) 

#Graph!
c <- confirmed_US_totals_long %>%
  filter(Province_State %in% ten_highest_confirmed_df$Province_State) %>%
  ggplot(aes(x = Date,  y = Confirmed)) + 
    geom_point() +
    geom_line() +
    ggtitle("Top 10 US States by Total Confirmed Cases") +
    facet_wrap(~Province_State) +
    transition_reveal(Date) 
animate(c, end_pause = 15)